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I find this very weird as i have never experienced anything like this before as you can see from the way i run the java programs i always redefine the classpath so why this is happening is really alien to me.

Sounds like user error.
How are you sure that the two programs with the same name are different and that the one in the JPProcTim folder is being executed?
Could the JProc.class files be the same in the two folders?
What happens if you rename the .class file you don't want executed to say .xxx and then execute the java command?
The line you posted

What is motivating you to name classes this way? Is this some kind of version control?

There's no motivation. Its something i stumbled upon and found very weird and was thinking it was somethin wrong i was doing but it seems weird that the intrepreter would react in this way. Its not part of any version control.

Originally Posted by nspils

Perhaps it is time to change the structure of your directories, or your file names, until you hit on a "final" version, then do your final builds.

Perhaps you are right about this and i have to have different names for all my classes.